About the Authors

Mitchell Guttman

To whom correspondence should be addressed. E-mail: mguttman@mit.edu

¤ Current address: Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America

Affiliations Penn Center for Bioinformatics, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America , Department of Pathology and Laboratory Medicine, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, United States of America

Carolyn Mies

Affiliation Department of Pathology and Laboratory Medicine, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, United States of America

Katarzyna Dudycz-Sulicz

Affiliation Department of Pathology and Laboratory Medicine, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, United States of America

Sharon J Diskin

Affiliation Division of Oncology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America

Don A Baldwin

Affiliation Penn Microarray Facility, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America

Christian J Stoeckert Jr.

Affiliations Penn Center for Bioinformatics, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America , Department of Genetics. University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, United States of America

Gregory R Grant

Affiliations Penn Center for Bioinformatics, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America , Department of Genetics. University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, United States of America

Competing Interests

The authors have declared that no competing interests exist.

Author Contributions

MG and GRG conceived of and designed the MSA algorithm and the CGH-MSA software package. MG implemented the MSA algorithm and coded the CGH-MSA software package MG, CM, KDS, DAB, and GRG contributed to the design of the experiments described in this study. KDS performed the Array CGH experiments and Laser Capture Microdissection. CM provided the samples and differentiated the cases into appropriate pathological classifications. SJD provided computational insights, helpful feedback, and access to the STAC source code. CJS provided project guidance and support. MG and GRG optimized the STAC algorithm for use in MSA. MG and GRG developed the simulation model. MG and GRG wrote the paper.